MolNFT v1 · #128007 · RNA

The structure of the G. violaceus guanidine II riboswitch P2 stem-loop

5NDH · RNA (5'-R(*GP*(CBV) P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP…: “The structure of the G. violaceus guanidine II riboswitch P2 stem-loop”. X-ray diffraction, 4 ligands (GAI, NA, MG). MolNFT v1 #128007 on GenesisL1: 3D structure…

PDB: 5NDH
Type: RNA
Length: 64 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*GP*(CBV) P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3')
Ligands: GAI, NA, MG, SO4

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA (5'-R(GP(CBV) PGPGPGPGPAPCPGPAPCPCPCPCPGPC)-3')	rna	16	—	—

Ligands and binding sites

GAI · Guanidine · ligand · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 4 copies · chains A, B, C
MG · Magnesium ion · metal · chains A
SO4 · Sulfate ion · ion · 2 copies · chains B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

3 interfaces between chains.

A–C · 345 Å² buried · 21 hydrogen bonds · nucleic-nucleic
B–D · 338 Å² buried · 19 hydrogen bonds · nucleic-nucleic
B–C · 194 Å² buried · 7 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

5NDH · The structure of the G. violaceus guanidine II riboswitch P2 stem-loop · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5NDH · PDBe 5NDH

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.